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- PDB-1ipf: TROPINONE REDUCTASE-II COMPLEXED WITH NADPH AND TROPINONE -

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Basic information

Entry
Database: PDB / ID: 1ipf
TitleTROPINONE REDUCTASE-II COMPLEXED WITH NADPH AND TROPINONE
ComponentsTROPINONE REDUCTASE-II
KeywordsOXIDOREDUCTASE / TROPANE ALKALOID BIOSYNTHESIS / REDUCTION OF TROPINONE TO PSEUDOTROPINE / SHORT-CHAIN DEHYDROGENASE / TROPINONE / LAUE DIFFRACTION / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


tropinone reductase II / tropinone reductase activity / tropane alkaloid biosynthetic process
Similarity search - Function
Tropinone reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / 8-METHYL-8-AZABICYCLO[3,2,1]OCTAN-3-ONE / Tropinone reductase 2
Similarity search - Component
Biological speciesDatura stramonium (jimsonweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsYamashita, A. / Endo, M. / Higashi, T. / Nakatsu, T. / Yamada, Y. / Oda, J. / Kato, H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: BIOCHEMISTRY / Year: 2003
Title: Capturing Enzyme Structure Prior to Reaction Initiation: Tropinone Reductase-II-Substrate Complexes
Authors: Yamashita, A. / Endo, M. / Higashi, T. / Nakatsu, T. / Yamada, Y. / Oda, J. / Kato, H.
#1: Journal: Biochemistry / Year: 1999
Title: Structure of Tropinone Reductase-II Complexed with NADP+ and Pseudotropine at 1.9 A Resolution: Implication for Stereospecific Substrate Binding and Catalysis
Authors: Yamashita, A. / Kato, H. / Wakatsuki, S. / Tomizaki, T. / Nakatsu, T. / Nakajima, K. / Hashimoto, T. / Yamada, Y. / Oda, J.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Crystal Structures of Two Tropinone Reductases: Different Reaction Stereospecificities in the Same Protein Fold
Authors: Nakajima, K. / Yamashita, A. / Akama, H. / Nakatsu, T. / Kato, H. / Hashimoto, T. / Oda, J. / Yamada, Y.
History
DepositionMay 9, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TROPINONE REDUCTASE-II
B: TROPINONE REDUCTASE-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1866
Polymers56,4172
Non-polymers1,7694
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-13 kcal/mol
Surface area20450 Å2
MethodPISA
2
A: TROPINONE REDUCTASE-II
B: TROPINONE REDUCTASE-II
hetero molecules

A: TROPINONE REDUCTASE-II
B: TROPINONE REDUCTASE-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,37112
Polymers112,8334
Non-polymers3,5388
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area21840 Å2
ΔGint-106 kcal/mol
Surface area31010 Å2
MethodPISA
3
A: TROPINONE REDUCTASE-II
hetero molecules

B: TROPINONE REDUCTASE-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1866
Polymers56,4172
Non-polymers1,7694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area6950 Å2
ΔGint-22 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.600, 88.600, 337.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-295-

HOH

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Components

#1: Protein TROPINONE REDUCTASE-II


Mass: 28208.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Datura stramonium (jimsonweed) / Organ: CULTURED ROOT / Plasmid: PETTR2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P50163, tropinone reductase II
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-TNE / 8-METHYL-8-AZABICYCLO[3,2,1]OCTAN-3-ONE / TROPINONE / TROPINONE


Mass: 139.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13NO / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: lithium sulfate, dithiothreitol, HEPES, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K
Crystal grow
*PLUS
Method: unknown
Details: Petsko, G.A., (2000) Curr. Opin. Chem. Biol., 4, 89.

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.7-1.65
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 11, 1998
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
10.71
21.651
ReflectionResolution: 2.5→37 Å / Num. all: 24958 / Num. obs: 24567 / % possible obs: 86.5 % / Observed criterion σ(I): 1 / Redundancy: 6.34 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.134
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.27 / % possible all: 84.3
Reflection
*PLUS
Lowest resolution: 9999 Å / Num. measured all: 155667
Reflection shell
*PLUS
% possible obs: 84.3 % / Rmerge(I) obs: 0.27

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Processing

Software
NameVersionClassification
INTLAUEdata collection
LAUENORMdata reduction
X-PLOR3.851model building
X-PLOR3.851refinement
INTLAUEdata reduction
LAUENORMdata scaling
X-PLOR3.851phasing
RefinementStarting model: PDB ENTRY 2AE2

2ae2


Resolution: 2.5→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: HOH 61, WHICH IS LISTED IN REMARK 525, MAKES A 3.55 A HYDROGEN BOND WITH HOH 11, WHICH MAKES A HYDROGEN BOND WITH PROTEIN MOLECULE AT 2.91 A DISTANCE.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1193 5 %RANDOM
Rwork0.197 ---
obs-23323 84.1 %-
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 116 62 4128
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.33
X-RAY DIFFRACTIONx_dihedral_angle_d23.81
X-RAY DIFFRACTIONx_improper_angle_d0.685
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.388 131 3.85 %
Rwork0.252 2509 -
obs-2903 77.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2NPH.PARAMTOPH19.SOL
X-RAY DIFFRACTION3TPO.PARAMNPH.TOP
X-RAY DIFFRACTION4TPO.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.332
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.812
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.685

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